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An LTR retrotransposon insertion was the cause of world’s first low erucic acid Brassica rapa oilseed cultivar

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Abstract

Brassica rapa is an important oilseed crop species next to B. napus in Brassicaceae. However, genetic improvement of B. rapa oilseeds has not been intensively conducted compared to B. napus, which resulted in the limited number of low erucic acid (LEA) cultivars, which is an essential trait for edible oil materials. Candle and Tobin are LEA B. rapa cultivars bred in Canada that are closely related to each other; however, the causal mutation has not been identified. This study was initially aimed to investigate whether the alleles of BrFAE1, the gene encoding a key enzyme for erucic acid synthesis, in Candle and Tobin have mutations impairing their functions. An insertion of the long terminal repeat (LTR) retrotransposon, designated as BRACOPIA, was identified in the 5′ end of the coding region of the gene in both Candle and Tobin. BRACOPIA disrupted the transcription in developing seeds, resulting in a loss of function allele designated as brfae1re. Next, we found that Span, the world’s first LEA B. rapa cultivar developed in Canada, has brfae1re, suggesting that the BRACOPIA insertion is the founder mutation of Canadian LEA B. rapa cultivars. Finally, we investigated the distribution of BRACOPIA family retrotransposons in the Brassica genus, and found that they are present in both the A and C genomes, but the activity has been kept rather modest. Since brfae1re is easily distinguishable from the wild-type allele by PCR, the identification of this mutation could enhance LEA breeding in B. rapa.

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Abbreviations

LEA:

Low erucic acid

HEA:

High erucic acid

LTR:

Long terminal repeat

BRACOPIA :

Brassica rapa Copia retrotransposon

BOLCOPIA :

Brassica oleracea Copia retrotransposon

BNACOPIA :

Brassica napus Copia retrotransposon

FAE1 :

FATTY ACID ELONGATION 1

VLCFA:

Very long-chain fatty acids

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Acknowledgments

Authors would like to thank Dr. Christina Eynck for proving Canadian B. rapa cultivars; Dr. Fengqun Yu for her generous support to conduct DNA experiments with these cultivars at Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada (AAFC); and Dr. Mohammad Shakhawat Hossain, Oilseed Research Centre, Bangladesh Agricultural Research Institute (BARI), for his support to the fatty acid composition analysis.

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Authors and Affiliations

  1. Graduate School of Science and Technology, Niigata University, 2-8050, Ikarashi, Nishi-ku, Niigata, 950-2181, Japan

    Eigo Fukai, Daniel J. Shea, Taketo Funaki & Keiichi Okazaki

  2. Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada (AAFC), 107 Science Place, Saskatoon, SK, S7N 0X2, Canada

    Md. Masud Karim & Kevin C. Falk

  3. Department of Plant Pathology, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka, 1207, Bangladesh

    Nazmoon Naher Tonu

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  1. Eigo Fukai
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Kevin C. Falk retired.

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Fig. S1 Functional domains predicted on the ORF of BRACOPIA. Domains were indicated as boxes marked with different patterns with each of names. LTR; Long Terminal Repeat, GAG; GAG polyprotein, GAG-pre-integrase; upstream region of integrase, rve; integrase core domain, RVT; Reverse transcriptase core domain.

Fig. S2 Comparison of ORFs of the BrFAE1 alleles. Nucleotide differences compared to the ORF of BrFAE1 in HEA Tori-7 were indicated as lines, with positional information from translation start site (+ 1) in each ORF. In parentheses, amino-acid changes deduced by the nucleotide substitutions were indicated. N-terminal region specific to ORF of brfae1re was indicated as a grey box. Please note that the low functionalities of the alleles of two LEA B. rapa cultivars, brfae1.1 (Sanjiecaizi) and brfae1.2 (HJa 96368) are attributed to their low transcription level associated with a 28bp deletion found in their promoter sequences (Yan et al. 2015). Sequences used are LC053834 for BrFAE1 (Tori-7), BnaA08g11130D for bnfae1.1 (Darmor-bzh), KF999615 for brfae1.1 (Sanjiecaizi), KF999623 for brfae1.2 (HJa 96368), and LC053835 and LC053837 for brfae1re in Candle and Tobin, respectively.

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Fukai, E., Karim, M.M., Shea, D.J. et al. An LTR retrotransposon insertion was the cause of world’s first low erucic acid Brassica rapa oilseed cultivar. Mol Breeding 39, 15 (2019). https://doi.org/10.1007/s11032-018-0916-9

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